Pathway Analysis of DEGs Using MapMan
Metabolic pathways analysis of DEGs was performed through MapMan to
determine the effects of drought stress in root tissues of soybean. In
our data, out of all up- and down-regulated DEGs of DTP and DSP, only
121 and 105 DEGs, respectively were mapped, and out of them only 99 and
87 were shown in Fig. 7B , whereas only 123 and 123 DEGs were
mapped out of all up- and down-regulated DEGs of DTL and DSL,
respectively, and 101 and 101were presented in the Fig. 7A by
using Gmax_AFFY_09.m02 (Thimm et al., 2004). Comprehensive overview of
DEGs, such as peroxidases, TFs, secondary metabolites, PRs, cell wall,
signaling, hormone signaling, redox state etc. are presented inFig. 7A&B . Both MapMan and GO analysis are in well agreement,
as in both cases DEGs enrichment were found similar in pathways and
functional groups. However, most of the DEGs were assigned to specific
functional groups, genes relevant to the terms hormone signaling, cell
wall, antioxidant activity, signaling, proteolysis, TFs (MYB, ERF, WRKY,
bZIP, and bHLH) were highly expressed in tolerant genotypes, and reverse
trend was observed in sensitive genotypes.
Hence, consistency of GO and MapMan analyses revealed that drought
stress response was highly enriched in the DEGs associated with water
transport (GO:0006833), cell wall (GO:0005618), plant-type vacuole
membrane (GO:0000325), antioxidant activity (GO:0016209), peroxidase
activity (GO:0004601), catalytic-activity (GO:0003824), auxin transport
(GO:0060918), protein-kinase activity (GO:0004672), secondary metabolite
synthesis (GO:0044550), transcription-factor activity (GO:0003700),
hormone-signaling (GO:0009755). Hence, these terms can play vital role
in regulating drought stress tolerance at germination stage in soybean.
KEGG Pathway Analysis of DEGs
Involved in Secondary Metabolism and Hormone-Mediated Signaling
Based on the GO and MapMan analysis as well as previous literature,
secondary metabolites and hormone-mediated signaling plays important
role in drought tolerance. Hence, DEGs related to secondary metabolites
and hormone-mediated signaling were further subjected to KEGG pathway
enrichment analysis. Our results showed that genes associated with
biosynthesis of secondary metabolites such as shikimate acid, alkaloid,
anthocyanin, lignin, flavonoids and terpenoid were mainly differentially
expressed under drought stress in root tissues (Table 2). The
number of up- and down-regulated genes associated with secondary
metabolites biosynthesis such as shikimate acid, alkaloid, anthocyanin,
lignin and terpenoid in both tolerant and sensitive genotypes are
presented (Fig. S1; Table S8).
Furthermore, many DEGs related to AUX, ABA, GA, JA, ETH and
Brassinosteroid (BR) were found in drought stressed soybean roots. The
changes in the gene expressions of hormoneāresponsive genes, and their
regulating TFs are shown in Table 3. To further understand the
regulation of phytohormone in soybean transcriptome, several DEGs
related to the biosynthesis of phytohormones viz., AUX, ABA, GA, JA, ETH
and BR were identified under drought stress in the soybean root tissues.
The changes in the gene expressions of hormoneāresponsive genes, and
their regulating TFs are presented (Table 3; Fig. S2) . The
number of DEGs involved in the hormonal-signaling were mostly related to
AUX followed by GA, ETH and ABA (Table S13). This indicates
important role of these hormones especially AUX in drought stress
response at germination stage.